Nonequilibrium landscape theory of neural networks
Han Yan, Lei Zhao, Liang Hu, Xidi Wang, Erkang Wang, and Jin Wang
The brain map project aims at mapping out human brain neuron connections. Even with given wirings, the global and physical understandings of the function and behavior of the brain are still challenging. Learning and memory processes were previously globally quantified for symmetrically connected neural networks. However, realistic neural networks of cognitive processes and physiological rhythm regulations are asymmetrically connected. We developed a nonequilibrium landscape–flux theory for asymmetrically connected neural networks. We found (pp. E4185–E4194) the landscape topography is critical in determining the global stability and function of the neural networks. The cognitive dynamics is determined by both landscape gradient and flux. For rapid-eye movement sleep cycles, we predicted the key network wirings based on landscape topography, in agreement with experiments.
Prediction and experimental validation of enzyme substrate specificity in protein structures
Shivas R. Amin, Serkan Erdin, R. Matthew Ward, Rhonald C. Lua, and Olivier Lichtarge
Many proteins solved by Structural Genomics have low sequence identity to other proteins and cannot be assigned functions. To address this problem, we present (pp. E4195–E4202) a computational approach that creates structural motifs of a few evolutionarily important residues, and these motifs probe local geometric and evolutionary similarities in other protein structures to detect functional similarities. This approach does not require prior knowledge of functional mechanisms and is highly accurate in computational benchmarks when annotations rely on homologs with low sequence identity. We further demonstrate the accuracy of this approach using biochemical and mutagenesis studies to validate two predictions of unannotated proteins.
Autophosphorylation and Pin1 binding coordinate DNA damage-induced HIPK2 activation and cell death
Nadja Bitomsky, Elisa Conrad, Christian Moritz, Tilman Polonio-Vallon, Dirk Sombroek, Kathrin Schultheiss, Carolina Glas, Vera Greiner, Christoph Herbel, Fiamma Mantovani, Giannino del Sal, Francesca Peri, and Thomas G. Hofmann
Activation of the cell death (apoptosis) program is a major principle of DNA-damaging cancer treatments including ionizing radiation and chemotherapeutic drug treatment. The protein kinase HIPK2 plays a key role in radiosensitivity and chemosensitivity. Here (pp. E4203–E4212), we found that HIPK2 autointeracts and autophosphorylates after DNA damage. HIPK2 autophosphorylation is conserved in evolution and regulates its apoptosis-inducing activity by facilitating binding of the isomerase Pin1. Pin1 couples HIPK2 activation to its stabilization and is essential for DNA damage-induced apoptosis in cancer cells and in zebrafish. Our findings identify a mechanism linking HIPK2 activation to its stabilization and highlight a conserved function of HIPK2 and Pin1 in the DNA damage-induced apoptosis response.
Monoallelic loss of tumor suppressor GRIM-19 promotes tumorigenesis in mice
Sudhakar Kalakonda, Shreeram C. Nallar, Sausan Jaber, Susan K. Keay, Ellen Rorke, Raghava Munivenkatappa, Daniel J. Lindner, Gary M. Fiskum, and Dhananjaya V. Kalvakolanu
Gene-associated with retinoid-interferon induced mortality-19 (GRIM-19) is an interferon-retinoid–regulated growth suppressor that inhibits cell growth by targeting the transcription factor STAT3 for inhibition. In primary human tumors GRIM-19 is suppressed or mutated, leading to constitutive STAT3 activity and indicating the tumor-suppressive function of GRIM-19. To understand the in vivo role of Grim-19 in tumor development, we generated a Grim-19 conditional knockout mouse. We found (pp. E4213–E4222) that deletion of even a single Grim-19 allele is sufficient to augment skin tumorigenesis in mice, thus establishing a critical role for Grim-19 as a tumor suppressor. Tumors that developed in the absence of Grim-19 exhibited mitochondrial respiratory chain dysfunction, elevated glycolysis, and Stat3-responsive gene expression.
Genome duplication and mutations in ACE2 cause multicellular, fast-sedimenting phenotypes in evolved Saccharomyces cerevisiae
Bart Oud, Victor Guadalupe-Medina, Jurgen F. Nijkamp, Dick de Ridder, Jack T. Pronk, Antonius J. A. van Maris, and Jean-Marc Daran
The shift from unicellular to multicellular life forms represents a key innovation step in the evolution of life on Earth. However, knowledge on the evolutionary pressures resulting in the selection of multicellular life forms and the underlying molecular mechanisms is far from complete. Our study (pp. E4223–E4231) provides a complete identification of the specific genetic changes by which the unicellular eukaryote S. cerevisiae can acquire a multicellular, fast-sedimenting phenotype. We demonstrated that a minimal evolutionary mechanism encompassed a deregulation of the late step of the cell cycle through mutation in ACE2 followed by whole genome duplication.
Natural killer cell licensing in mice with inducible expression of MHC class I
Takashi Ebihara, A. Helena Jonsson, and Wayne M. Yokoyama
Natural killer (NK) cells undergo a licensing (or education) process through interactions with their MHC class I-specific receptors and self-MHC class I to become functionally competent. Previously it was not possible to study the acute consequences of these interactions. We developed transgenic mice (pp. E4232–E4237) to induce MHC class I acutely in an otherwise MHC class I-deficient environment. In these mice, acute NK cell licensing is dependent on interactions between NK-cell receptors and other hematopoietic cells; the acute process did not appear to induce detectable differences in the licensed NK cells themselves.
Isolation and characterization of the positive-sense replicative intermediate of a negative-strand RNA virus
Ashley York, Narin Hengrung, Frank T. Vreede, Juha T. Huiskonen, and Ervin Fodor
The negative-strand RNA viruses comprise several significant human, animal, and plant pathogens that have considerable health and economic impact globally. During infection, replication of the single-stranded negative-sense RNA genome occurs through a complementary RNA intermediate, which is believed to complex with viral proteins to form a complementary ribonucleoprotein (cRNP). The isolation of these complexes from infected cells has never been accomplished, greatly hampering our understanding of genome replication. We report (pp. E4238–E4245) a technological advance for the isolation of this elusive but essential component of the influenza A virus replication machine. Structural and functional characterization of the influenza A virus cRNP has led to the proposal of a model of genome replication that relies on a trans-activating viral RNA-dependent RNA polymerase.
Charge-dependent secretion of an intrinsically disordered protein via the autotransporter pathway
Wanyoike Kang’ethe, and Harris D. Bernstein
Bacterial autotransporter proteins contain a large segment that is transported from the periplasm (the space between the inner and outer membranes) to the extracellular milieu. Because the periplasm lacks ATP, the energy required for the transport reaction is thought to be derived from the folding of this segment following its secretion. Contrary to the prevailing view, we found (pp. E4246–E4255) that a heterologous polypeptide that cannot fold was secreted efficiently when it was fused to an autotransporter. Reducing the negative charge of this polypeptide, however, strongly impaired secretion. Our results identify net charge as a potentially important factor that drives autotransporter secretion.
Nitrite produced by Mycobacterium tuberculosis in human macrophages in physiologic oxygen impacts bacterial ATP consumption and gene expression
Amy Cunningham-Bussel, Tuo Zhang, and Carl F. Nathan
Most people infected with Mycobacterium tuberculosis (Mtb) suppress the pathogen’s replication without eradicating it. It is unknown how Mtb survives for decades in a hostile host environment. Respiration of nitrate to nitrite could help Mtb survive in hypoxic tissues but was not thought to be significant at physiologic oxygen tensions, nor was the resultant nitrite considered consequential to Mtb’s physiology. We found (pp. E4256–E4265) that Mtb infecting human macrophages in vitro produces copious nitrite at physiologic oxygen tensions. This slows Mtb’s growth and consumption of ATP and remodels its transcriptome differently than nitric oxide. Thus, respiration of nitrate and adaptation to nitrite are likely to play a prominent role in Mtb’s pathophysiology, whether or not the Mtb resides in hypoxic sites.
High-throughput imaging of neuronal activity in Caenorhabditis elegans
Johannes Larsch, Donovan Ventimiglia, Cornelia I. Bargmann, and Dirk R. Albrecht
Most behaviors and neuronal responses are variable across individual animals and repeated presentation of the same stimulus. Current neuronal recording techniques examine one animal at a time, whereas hundreds to thousands of trials may be necessary to understand the probability and range of responses. We developed (pp. E4266–E4273) an imaging system to record neuronal activity, detected by genetically encoded calcium indicators, simultaneously from 20 Caenorhabditis elegans animals in microfluidic arenas. We used this system to characterize chemosensory neuron responses to odors and pharmacological manipulation. The system allowed recordings in freely moving animals, whose neuronal responses could be correlated with behavior. We found that behavioral variability is observed even when sensory responses are reproducible, and that sensitivity to specific odors varies among individual animals.